Applications of ENCODE data to systematic analyses via data integration

Abstract

Large-scale genomic data have been utilized to generate unprecedented biological findings and new hypotheses. To delineate functional elements in the human genome, the Encyclopedia of DNA Elements (ENCODE) project has generated an enormous amount of genomic data, yielding around 7,000 data profiles in different cell and tissue types. In this article, we reviewed the systematic analyses that have integrated ENCODE data with other data sources to reveal new biological insights, ranging from human genome annotation to the identification of new candidate drugs. These analyses demonstrate the critical impact of ENCODE data on basic biology and translational research.

Computational modeling of chromatin accessibility identified important epigenomic regulators

“…To construct integrative models to predict chromatin accessibility, we utilized the GM12878 and HepG2 cell lines, for which high quality chromatin accessibility, TF binding and histone modification have been generated by the Encyclopedia of DNA elements (ENCODE) project [ 50 ]. The chromatin accessibility data were obtained by using the ATAC-seq, DNase-seq and FAIRE-seq experiments and downloaded from the ENCODE database as bedgraph files.…”

Computational Modeling of Chromatin Accessibility Identified Important Epigenomic Regulators

“…To construct integrative models to predict chromatin accessibility, we utilized the GM12878 and HepG2 cell lines, for which high quality chromatin accessibility, TF binding and histone modi cation have been generated by the Encyclopedia of DNA elements (ENCODE) project [39]. The chromatin accessibility data were obtained by using the ATAC-seq, DNase-seq and FAIRE-seq experiments and downloaded from the ENCODE database as bedgraph les.…”